Contacts of the strand formed by residues 31 - 39 (chain L) in PDB entry 2FRV
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 31 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344D LYS* 2.8 34.4 - - - +
27L VAL* 3.4 5.7 - - - +
28L GLU* 3.1 31.0 + - + +
29L GLY* 3.1 11.6 - - - +
30L GLY* 1.3 86.1 - - - +
32L ILE* 1.3 68.7 - - - +
33L LYS* 3.2 1.6 + - - +
508L GLY* 3.3 28.7 - - - +
509L THR 3.2 4.3 - - - +
510L PRO* 4.1 8.5 - - + -
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Residues in contact with ILE 32 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25L VAL* 4.1 15.0 - - + -
26L GLU 3.5 5.2 - - - -
27L VAL* 4.5 3.6 - - + -
31L LYS* 1.3 74.1 - - - +
33L LYS* 1.3 56.8 + - - +
34L ASN 3.4 25.1 - - - +
506L LEU* 3.1 41.3 - - + +
507L ILE* 3.7 5.6 - - - +
508L GLY* 2.8 24.1 + - - +
509L THR* 2.8 40.0 + - + +
511L ILE* 3.5 26.2 - - + -
520L ILE* 3.7 20.6 - - + -
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Residues in contact with LYS 33 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26L GLU* 2.7 49.3 + - + +
27L VAL 4.8 0.2 - - - -
28L GLU* 3.6 45.8 - - + +
31L LYS* 3.2 1.7 + - + +
32L ILE* 1.3 73.0 - - - +
34L ASN* 1.3 61.0 + - + +
507L ILE* 3.9 17.8 - - - +
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Residues in contact with ASN 34 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25L VAL* 3.5 0.7 - - - -
26L GLU* 3.2 36.5 + - - +
32L ILE* 3.4 8.6 - - - +
33L LYS* 1.3 81.2 - - + +
35L ALA* 1.3 82.8 + - - +
36L TRP* 3.7 29.2 - - + -
493L ARG* 2.8 28.2 + - - +
499L LEU* 4.2 8.1 - - - +
507L ILE* 4.0 5.6 - - - -
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Residues in contact with ALA 35 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24L GLU 3.6 2.5 - - - -
25L VAL* 4.0 5.4 - - + -
32L ILE* 4.3 0.7 - - + -
34L ASN* 1.3 93.3 + - - +
36L TRP* 1.3 61.7 + - - +
493L ARG* 2.7 31.4 + - - -
499L LEU* 4.8 0.2 - - - +
503L GLU* 3.6 22.7 - - - +
506L LEU* 3.8 39.3 - - + -
507L ILE* 4.0 3.6 - - + +
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Residues in contact with TRP 36 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8L LYS* 4.6 11.4 - - + -
22L ARG 4.1 0.2 - - - +
23L ILE* 3.8 8.5 - - - +
24L GLU* 3.0 62.8 + - + +
25L VAL* 4.2 2.0 - - - -
26L GLU* 3.7 39.3 - - + -
34L ASN* 3.7 24.0 - - + -
35L ALA* 1.3 85.1 - - - +
37L SER* 1.3 60.8 + - - +
38L MET* 3.8 9.2 + - + +
349L HIS* 3.8 27.8 + + + -
354L TYR* 4.0 22.0 - + + -
493L ARG* 3.1 26.9 - - - +
503L GLU* 3.5 6.1 - - - -
506L LEU* 6.2 0.4 - - - -
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Residues in contact with SER 37 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21L LEU* 3.7 14.0 - - - +
22L ARG 4.2 1.8 - - - -
23L ILE* 4.3 8.0 - - - +
36L TRP* 1.3 69.8 - - - +
38L MET* 1.3 61.5 + - - +
39L SER* 4.0 0.4 + - - -
354L TYR* 3.4 16.0 - - - -
355L SER* 3.9 10.0 + - - -
490L LEU* 2.8 33.1 + - - +
491L GLY 4.5 0.4 - - - -
492L PRO* 4.7 1.0 - - - +
502L VAL* 3.7 25.5 - - - +
503L GLU* 2.9 17.8 + - - +
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Residues in contact with MET 38 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21L LEU* 3.4 3.6 - - - +
22L ARG* 2.7 63.3 + - + +
24L GLU* 3.4 35.2 - - - +
36L TRP* 4.1 7.6 - - + +
37L SER* 1.3 75.9 + - - +
39L SER* 1.3 61.1 + - - +
40L THR* 3.7 4.1 - - + +
327L TRP* 4.6 0.9 - - + -
348L PHE* 3.6 43.7 - - + -
349L HIS* 3.9 16.6 - - + +
354L TYR* 3.4 35.0 - - + +
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Residues in contact with SER 39 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20L HIS 3.7 5.2 - - - -
21L LEU* 4.1 8.7 - - - +
38L MET* 1.3 70.8 - - - +
40L THR* 1.3 58.2 + - - +
41L LEU 3.8 1.8 - - - -
327L TRP* 3.6 5.7 - - - -
355L SER* 3.3 17.7 + - - -
356L TRP* 3.3 26.4 + - - -
357L MET* 3.4 27.3 - - - +
490L LEU 4.3 3.6 + - - -
531L ILE* 3.7 19.1 - - - +
535L VAL* 3.7 17.3 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il